Chain or wheel bearing issue

[darrsi]

Wheel alignment is spot on. Aligned perfectly to the markings on the trailing arm. Just to double check I ran a piece of string around the back wheel up to the front of the bike parallel to the front wheel, all good.

I am I right in thinking the OEM front sprocket had some kind of rubber vibration damping device? If so, the JT sprocket doesn't have this - would it effect the alignment of the sprocket?

I've never had that, but i very much doubt it.
With the bike on the centre stand just spin the rear wheel by hand, it should make a purring sound with no clunking, screeching or inconsistent noises. You'll know if it's right or wrong.
If the wheel is misaligned the chain will try to correct itself on the front sprocket creating nasty noises, which will be more noticeable when riding but should be easy enough to hear when moving by hand as well.